ID code: '2NLL' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 1393 C1' C C 502 beta 1389 1394 1392 1412 C1' A C 503 beta 1408 1413 1411 1433 C1' G C 504 beta 1429 1434 1432 1455 C1' G C 505 beta 1451 1456 1454 1477 C1' T C 506 beta 1473 1478 1476 1497 C1' C C 507 beta 1493 1498 1496 1516 C1' A C 508 beta 1512 1517 1515 1537 C1' T C 509 beta 1533 1538 1536 1557 C1' T C 510 beta 1553 1558 1556 1576 C1' 5IU C 511 beta 1581 1567 1577 1597 C1' C C 512 beta 1593 1598 1596 1616 C1' A C 513 beta 1612 1617 1615 1637 C1' G C 514 beta 1633 1638 1636 1659 C1' G C 515 beta 1655 1660 1658 1681 C1' T C 516 beta 1677 1682 1680 1701 C1' C C 517 beta 1697 1702 1700 1720 C1' A C 518 beta 1716 1721 1719 1741 C1' G C 519 beta 1737 1742 1740 1761 C1' C D 521 beta 1757 1762 1760 1780 C1' T D 522 beta 1776 1781 1779 1800 C1' G D 523 beta 1796 1801 1799 1822 C1' A D 524 beta 1818 1823 1821 1843 C1' C D 525 beta 1839 1844 1842 1862 C1' C D 526 beta 1858 1863 1861 1881 C1' T D 527 beta 1877 1882 1880 1901 C1' G D 528 beta 1897 1902 1900 1923 C1' A D 529 beta 1919 1924 1922 1944 C1' A D 530 beta 1940 1945 1943 1965 C1' A D 531 beta 1961 1966 1964 1986 C1' T D 532 beta 1982 1987 1985 2006 C1' G D 533 beta 2002 2007 2005 2028 C1' A D 534 beta 2024 2029 2027 2049 C1' C D 535 beta 2045 2050 2048 2068 C1' C D 536 beta 2064 2069 2067 2087 C1' T D 537 beta 2083 2088 2086 2107 C1' G D 538 beta 2103 2108 2106 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1392 C2' C C 502 1393 1390 1411 C2' A C 503 1412 1409 1432 C2' G C 504 1433 1430 1454 C2' G C 505 1455 1452 1476 C2' T C 506 1477 1474 1496 C2' C C 507 1497 1494 1515 C2' A C 508 1516 1513 1536 C2' T C 509 1537 1534 1556 C2' T C 510 1557 1554 1577 C2' 5IU C 511 1576 1578 1596 C2' C C 512 1597 1594 1615 C2' A C 513 1616 1613 1636 C2' G C 514 1637 1634 1658 C2' G C 515 1659 1656 1680 C2' T C 516 1681 1678 1700 C2' C C 517 1701 1698 1719 C2' A C 518 1720 1717 1740 C2' G C 519 1741 1738 1760 C2' C D 521 1761 1758 1779 C2' T D 522 1780 1777 1799 C2' G D 523 1800 1797 1821 C2' A D 524 1822 1819 1842 C2' C D 525 1843 1840 1861 C2' C D 526 1862 1859 1880 C2' T D 527 1881 1878 1900 C2' G D 528 1901 1898 1922 C2' A D 529 1923 1920 1943 C2' A D 530 1944 1941 1964 C2' A D 531 1965 1962 1985 C2' T D 532 1986 1983 2005 C2' G D 533 2006 2003 2027 C2' A D 534 2028 2025 2048 C2' C D 535 2049 2046 2067 C2' C D 536 2068 2065 2086 C2' T D 537 2087 2084 2106 C2' G D 538 2107 2104 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1390 C3' C C 502 OK 1388 1391 1392 1409 C3' A C 503 OK 1407 1410 1411 1430 C3' G C 504 OK 1428 1431 1432 1452 C3' G C 505 OK 1450 1453 1454 1474 C3' T C 506 OK 1472 1475 1476 1494 C3' C C 507 OK 1492 1495 1496 1513 C3' A C 508 OK 1511 1514 1515 1534 C3' T C 509 OK 1532 1535 1536 1554 C3' T C 510 OK 1552 1555 1556 1578 C3' 5IU C 511 OK 1579 1580 1577 1594 C3' C C 512 OK 1592 1595 1596 1613 C3' A C 513 OK 1611 1614 1615 1634 C3' G C 514 OK 1632 1635 1636 1656 C3' G C 515 OK 1654 1657 1658 1678 C3' T C 516 OK 1676 1679 1680 1698 C3' C C 517 OK 1696 1699 1700 1717 C3' A C 518 OK 1715 1718 1719 1738 C3' G C 519 OK 1736 1739 1740 1758 C3' C D 521 OK 1756 1759 1760 1777 C3' T D 522 OK 1775 1778 1779 1797 C3' G D 523 OK 1795 1798 1799 1819 C3' A D 524 OK 1817 1820 1821 1840 C3' C D 525 OK 1838 1841 1842 1859 C3' C D 526 OK 1857 1860 1861 1878 C3' T D 527 OK 1876 1879 1880 1898 C3' G D 528 OK 1896 1899 1900 1920 C3' A D 529 OK 1918 1921 1922 1941 C3' A D 530 OK 1939 1942 1943 1962 C3' A D 531 OK 1960 1963 1964 1983 C3' T D 532 OK 1981 1984 1985 2003 C3' G D 533 OK 2001 2004 2005 2025 C3' A D 534 OK 2023 2026 2027 2046 C3' C D 535 OK 2044 2047 2048 2065 C3' C D 536 OK 2063 2066 2067 2084 C3' T D 537 OK 2082 2085 2086 2104 C3' G D 538 OK 2102 2105 2106 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1388 C4' C C 502 OK 1390 1387 1389 1407 C4' A C 503 OK 1409 1406 1408 1428 C4' G C 504 OK 1430 1427 1429 1450 C4' G C 505 OK 1452 1449 1451 1472 C4' T C 506 OK 1474 1471 1473 1492 C4' C C 507 OK 1494 1491 1493 1511 C4' A C 508 OK 1513 1510 1512 1532 C4' T C 509 OK 1534 1531 1533 1552 C4' T C 510 OK 1554 1551 1553 1579 C4' 5IU C 511 OK 1578 1582 1581 1592 C4' C C 512 OK 1594 1591 1593 1611 C4' A C 513 OK 1613 1610 1612 1632 C4' G C 514 OK 1634 1631 1633 1654 C4' G C 515 OK 1656 1653 1655 1676 C4' T C 516 OK 1678 1675 1677 1696 C4' C C 517 OK 1698 1695 1697 1715 C4' A C 518 OK 1717 1714 1716 1736 C4' G C 519 OK 1738 1735 1737 1756 C4' C D 521 OK 1758 1755 1757 1775 C4' T D 522 OK 1777 1774 1776 1795 C4' G D 523 OK 1797 1794 1796 1817 C4' A D 524 OK 1819 1816 1818 1838 C4' C D 525 OK 1840 1837 1839 1857 C4' C D 526 OK 1859 1856 1858 1876 C4' T D 527 OK 1878 1875 1877 1896 C4' G D 528 OK 1898 1895 1897 1918 C4' A D 529 OK 1920 1917 1919 1939 C4' A D 530 OK 1941 1938 1940 1960 C4' A D 531 OK 1962 1959 1961 1981 C4' T D 532 OK 1983 1980 1982 2001 C4' G D 533 OK 2003 2000 2002 2023 C4' A D 534 OK 2025 2022 2024 2044 C4' C D 535 OK 2046 2043 2045 2063 C4' C D 536 OK 2065 2062 2064 2082 C4' T D 537 OK 2084 2081 2083 2102 C4' G D 538 OK 2104 2101 2103 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1387 C5' C C 502 1386 1388 1406 C5' A C 503 1405 1407 1427 C5' G C 504 1426 1428 1449 C5' G C 505 1448 1450 1471 C5' T C 506 1470 1472 1491 C5' C C 507 1490 1492 1510 C5' A C 508 1509 1511 1531 C5' T C 509 1530 1532 1551 C5' T C 510 1550 1552 1582 C5' 5IU C 511 1583 1579 1591 C5' C C 512 1590 1592 1610 C5' A C 513 1609 1611 1631 C5' G C 514 1630 1632 1653 C5' G C 515 1652 1654 1675 C5' T C 516 1674 1676 1695 C5' C C 517 1694 1696 1714 C5' A C 518 1713 1715 1735 C5' G C 519 1734 1736 1755 C5' C D 521 1754 1756 1774 C5' T D 522 1773 1775 1794 C5' G D 523 1793 1795 1816 C5' A D 524 1815 1817 1837 C5' C D 525 1836 1838 1856 C5' C D 526 1855 1857 1875 C5' T D 527 1874 1876 1895 C5' G D 528 1894 1896 1917 C5' A D 529 1916 1918 1938 C5' A D 530 1937 1939 1959 C5' A D 531 1958 1960 1980 C5' T D 532 1979 1981 2000 C5' G D 533 1999 2001 2022 C5' A D 534 2021 2023 2043 C5' C D 535 2042 2044 2062 C5' C D 536 2061 2063 2081 C5' T D 537 2080 2082 2101 C5' G D 538 2100 2102 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1402 P A C 503 distorted distorted 1391 1403 1404 1405 1423 P G C 504 distorted distorted 1410 1424 1425 1426 1445 P G C 505 distorted distorted 1431 1446 1447 1448 1467 P T C 506 distorted distorted 1453 1468 1469 1470 1487 P C C 507 distorted distorted 1475 1488 1489 1490 1506 P A C 508 distorted distorted 1495 1507 1508 1509 1527 P T C 509 distorted distorted 1514 1528 1529 1530 1547 P T C 510 distorted distorted 1535 1548 1549 1550 1584 P 5IU C 511 distorted distorted 1555 1585 1586 1583 1587 P C C 512 distorted distorted 1580 1588 1589 1590 1606 P A C 513 distorted distorted 1595 1607 1608 1609 1627 P G C 514 distorted distorted 1614 1628 1629 1630 1649 P G C 515 distorted distorted 1635 1650 1651 1652 1671 P T C 516 distorted distorted 1657 1672 1673 1674 1691 P C C 517 distorted distorted 1679 1692 1693 1694 1710 P A C 518 distorted distorted 1699 1711 1712 1713 1731 P G C 519 distorted distorted 1718 1732 1733 1734 1770 P T D 522 distorted distorted 1759 1771 1772 1773 1790 P G D 523 distorted distorted 1778 1791 1792 1793 1812 P A D 524 distorted distorted 1798 1813 1814 1815 1833 P C D 525 distorted distorted 1820 1834 1835 1836 1852 P C D 526 distorted distorted 1841 1853 1854 1855 1871 P T D 527 distorted distorted 1860 1872 1873 1874 1891 P G D 528 distorted distorted 1879 1892 1893 1894 1913 P A D 529 distorted distorted 1899 1914 1915 1916 1934 P A D 530 distorted distorted 1921 1935 1936 1937 1955 P A D 531 distorted distorted 1942 1956 1957 1958 1976 P T D 532 distorted distorted 1963 1977 1978 1979 1996 P G D 533 distorted distorted 1984 1997 1998 1999 2018 P A D 534 distorted distorted 2004 2019 2020 2021 2039 P C D 535 distorted distorted 2026 2040 2041 2042 2058 P C D 536 distorted distorted 2047 2059 2060 2061 2077 P T D 537 distorted distorted 2066 2078 2079 2080 2097 P G D 538 distorted distorted 2085 2098 2099 2100 ---------------------------------------------------------------------------------